control: tag -1 patch
* Paul Gevers:
> With a recent upload of python-intervaltree the autopkgtest of
> python-intervaltree-bio fails in testing when that autopkgtest is run
> with the binary packages of python-intervaltree from unstable. It passes
> when run with only packages from testing. In tabular form:
> pass fail
> python-intervaltree from testing 3.0.2-1
> python-intervaltree-bio from testing 1.0.1-2
> all others from testing from testing
Oops, my fault, sorry about that. And hooray for autopkgtests, I guess.
Apparently, the .search() method was removed in intervaltree-3.0.
Replacing all instances of .search(B,E) with .overlap(B,E) in the
intervalltree-bio test code makes the tests pass once more. Here's a
patch.
Cheers,
-Hilko
>From 1fef621d6ec368fbd51f82eecbf98376b69055d4 Mon Sep 17 00:00:00 2001
From: Hilko Bengen <ben...@debian.org>
Date: Sat, 26 Jan 2019 22:56:49 +0100
Subject: [PATCH] Replace all .search() calls with .overlap() in tests and
documentation
---
README.rst | 2 +-
intervaltree_bio/__init__.py | 10 +++++-----
tests/genomeintervaltree_test.py | 4 ++--
3 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/README.rst b/README.rst
index b0f249f..b5ee422 100644
--- a/README.rst
+++ b/README.rst
@@ -34,7 +34,7 @@ The core example is loading the transcription regions of the ``knownGene`` table
It is then possible to use the data structure to search known genes within given intervals::
- >> result = knownGene[b'chr1'].search(100000, 138529)
+ >> result = knownGene[b'chr1'].overlap(100000, 138529)
It is possible to load other UCSC tables besides ``knownGene`` or specify custom URL or file to read the table from.
Consult the docstring of the ``GenomeIntervalTree.from_table`` method for more details.
diff --git a/intervaltree_bio/__init__.py b/intervaltree_bio/__init__.py
index 083baca..ac8fe4d 100644
--- a/intervaltree_bio/__init__.py
+++ b/intervaltree_bio/__init__.py
@@ -125,10 +125,10 @@ class GenomeIntervalTree(defaultdict):
>>> gtree = GenomeIntervalTree.from_bed(BytesIO(data))
>>> len(gtree)
1732
- >>> assert gtree[b'chr10'].search(22610878) == set([Interval(22610878, 22611813, [b'.', b'1000', b'.', b'471.725544438908', b'-1', b'3.21510858105313', b'389']), Interval(22610878, 22611813, [b'.', b'791', b'.', b'123.885507169449', b'-1', b'3.21510858105313', b'596'])])
- >>> assert gtree[b'chr10'].search(22611813) == set([])
- >>> assert gtree[b'chr1'].search(145036590, 145036594) == set([Interval(145036593, 145037123, [b'.', b'247', b'.', b'38.6720804428054', b'-1', b'3.06233123683911', b'265'])])
- >>> assert gtree[b'chr10'].search(145036594, 145036595) == set([])
+ >>> assert gtree[b'chr10'].overlap(22610878) == set([Interval(22610878, 22611813, [b'.', b'1000', b'.', b'471.725544438908', b'-1', b'3.21510858105313', b'389']), Interval(22610878, 22611813, [b'.', b'791', b'.', b'123.885507169449', b'-1', b'3.21510858105313', b'596'])])
+ >>> assert gtree[b'chr10'].overlap(22611813) == set([])
+ >>> assert gtree[b'chr1'].overlap(145036590, 145036594) == set([Interval(145036593, 145037123, [b'.', b'247', b'.', b'38.6720804428054', b'-1', b'3.06233123683911', b'265'])])
+ >>> assert gtree[b'chr10'].overlap(145036594, 145036595) == set([])
'''
# We collect all intervals into a set of lists, and then put them all at once into the tree structures
@@ -187,7 +187,7 @@ class GenomeIntervalTree(defaultdict):
>> knownGene = GenomeIntervalTree.from_table()
>> len(knownGene)
82960
- >> result = knownGene[b'chr1'].search(100000, 138529)
+ >> result = knownGene[b'chr1'].overlap(100000, 138529)
>> len(result)
1
>> list(result)[0].data['name']
diff --git a/tests/genomeintervaltree_test.py b/tests/genomeintervaltree_test.py
index c016760..363ba9f 100644
--- a/tests/genomeintervaltree_test.py
+++ b/tests/genomeintervaltree_test.py
@@ -23,7 +23,7 @@ def test_knownGene(base_url):
knownGene_localurl = 'file:///%s' % os.path.abspath(knownGene_file)
knownGene = GenomeIntervalTree.from_table(url=knownGene_localurl, decompress=True) # Py3 downloads .gz files to local files with names not ending with .gz
assert len(knownGene) == 82960
- result = knownGene[b'chr1'].search(100000, 138529)
+ result = knownGene[b'chr1'].overlap(100000, 138529)
assert len(result) == 1
assert list(result)[0].data['name'] == b'uc021oeg.2'
@@ -33,7 +33,7 @@ def test_knownGene(base_url):
knownGene = GenomeIntervalTree.from_table(url=knownGene_localurl, mode='exons', decompress=True)
assert len(knownGene) == 742493
- result = list(knownGene[b'chr1'].search(134772, 140566))
+ result = list(knownGene[b'chr1'].overlap(134772, 140566))
assert len(result) == 3
assert result[0].data == result[1].data and result[0].data == result[2].data
--
2.19.1
